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[*]1. locate the worlds folder in the server folder
[*]2.Copy the "forcedchunks.dat" file and paste it in the folder of the world you wish to have pixelmon in
Source: viewtopic.php?f=85&t=12696
I believe that should work, as for the other mod/plugin, I am not too sure. All you have to do is trial and error, but if you can find some kind of plugin to force it to have the pixelmon "forcechunks.dat" automatically added to new worlds then you don't have to worry about manually doing it. Then again you could just make the worlds, put it in, and make no new worlds. But I have found a few servers that apparently have pixelmon and mystacraft all-in-one. So it seems possible.